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biopet.biopet
Commits
b443f31f
Commit
b443f31f
authored
Oct 10, 2014
by
Peter van 't Hof
Browse files
Changed name to commandName
parent
8ba5ac3e
Changes
3
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/BiopetExecutable.scala
View file @
b443f31f
...
...
@@ -17,7 +17,8 @@ object BiopetExecutable {
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
sage
.
Sage
,
nl
.
lumc
.
sasc
.
biopet
.
pipelines
.
basty
.
Basty
),
"tool"
->
List
(
nl
.
lumc
.
sasc
.
biopet
.
core
.
apps
.
WipeReads
)
nl
.
lumc
.
sasc
.
biopet
.
core
.
apps
.
WipeReads
,
nl
.
lumc
.
sasc
.
biopet
.
core
.
apps
.
BiopetFlagstat
)
)
/**
...
...
@@ -26,7 +27,7 @@ object BiopetExecutable {
def
main
(
args
:
Array
[
String
])
:
Unit
=
{
def
toBulletedList
(
m
:
List
[
MainCommand
],
kind
:
String
=
""
,
bullet
:
String
=
"-"
)
=
"Available %ss:\n "
.
format
(
kind
)
+
bullet
+
" "
+
m
.
map
(
x
=>
x
.
n
ame
).
sorted
.
mkString
(
"\n "
+
bullet
+
" "
)
"Available %ss:\n "
.
format
(
kind
)
+
bullet
+
" "
+
m
.
map
(
x
=>
x
.
commandN
ame
).
sorted
.
mkString
(
"\n "
+
bullet
+
" "
)
def
usage
(
module
:
String
=
null
)
:
String
=
{
if
(
module
!=
null
)
checkModule
(
module
)
...
...
@@ -53,7 +54,7 @@ object BiopetExecutable {
def
getCommand
(
module
:
String
,
name
:
String
)
:
MainCommand
=
{
checkModule
(
module
)
val
command
=
modules
(
module
).
find
(
p
=>
p
.
n
ame
.
toLowerCase
==
name
.
toLowerCase
)
val
command
=
modules
(
module
).
find
(
p
=>
p
.
commandN
ame
.
toLowerCase
==
name
.
toLowerCase
)
if
(
command
==
None
)
{
System
.
err
.
println
(
s
"ERROR: command '$name' does not exist in module '$module'\n"
+
usage
(
module
))
System
.
exit
(
1
)
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/MainCommand.scala
View file @
b443f31f
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.core
trait
MainCommand
{
lazy
val
n
ame
=
this
.
getClass
.
getSimpleName
lazy
val
commandN
ame
=
this
.
getClass
.
getSimpleName
.
split
(
"\\$"
).
last
def
main
(
args
:
Array
[
String
])
...
...
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/apps/WipeReads.scala
View file @
b443f31f
...
...
@@ -460,9 +460,9 @@ object WipeReads extends MainCommand {
val
usage
:
String
=
s
"""
|Usage: java -jar BiopetFramework.jar tool $
n
ame [options] -I input -l regions -o output
|Usage: java -jar BiopetFramework.jar tool $
commandN
ame [options] -I input -l regions -o output
|
|$
n
ame - Tool for reads removal from an indexed BAM file
|$
commandN
ame - Tool for reads removal from an indexed BAM file
|
|Positional arguments:
| -I,--inputBAM Input BAM file, must be indexed with
...
...
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